jeffwhite,
It depends upon what type of test is being run. But, in general, it should not affect the results of the testing, unless the water was contaminated with drugs (including the urine from someone else, if they were taking certain drugs).
Some chemical will make the tests invalid. So, if there was blue bowl cleaner or other chemcial cleaners, it may cause the test to become invalid.
So, again, if it was just water which has dirt or bacteria in it, it will not affect the test at all. If the water has drugs it in, including the urine or feces of someone taking drugs, then those drugs could show up in the test. If it had chemicals in it, it might invalidate the test.
So, unless you know exactly what was in the water, it is not possible to know what the outcome will be.